Variant report

Variant	rs12477836
Chromosome Location	chr2:36646343-36646344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36646028..36647836-chr2:36650769..36652474,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10178804	1.00[CHB][hapmap]
rs10186135	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203010	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124514	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11124515	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124516	0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1159133	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12465282	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12465297	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12994926	0.93[AMR][1000 genomes]
rs13394052	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13407488	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2689711	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2689714	0.89[ASN][1000 genomes]
rs3755214	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770913	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770924	0.92[CEU][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770932	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770936	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3770946	0.90[GIH][hapmap];1.00[JPT][hapmap]
rs3770947	0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4233914	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670547	1.00[CHB][hapmap]
rs4670554	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6711707	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6755048	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs711255	1.00[JPT][hapmap]
rs7589917	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs848508	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs848509	0.89[ASN][1000 genomes]
rs848513	1.00[JPT][hapmap]
rs848514	1.00[JPT][hapmap]
rs888075	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs888076	0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs9308991	1.00[CHB][hapmap]
rs9308992	1.00[CHB][hapmap]
rs997602	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2756915	chr2:36622906-36657305	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2759041	chr2:36622906-36657305	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12477836	PRKD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36632200-36648000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:36635800-36647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:36636000-36647600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:36636000-36647600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:36636800-36647600	Weak transcription	Lung	lung
6	chr2:36636800-36656000	Weak transcription	Esophagus	oesophagus
7	chr2:36638000-36647800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:36638200-36647600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:36638400-36646400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:36639400-36647600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:36639600-36646600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:36639600-36647600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:36639600-36647800	Weak transcription	Spleen	Spleen
14	chr2:36640000-36656000	Genic enhancers	A549	lung
15	chr2:36640200-36653400	Genic enhancers	HUVEC	blood vessel
16	chr2:36640200-36680000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:36640400-36646800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:36640400-36647000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr2:36640400-36647200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:36640800-36646400	Strong transcription	HSMM	muscle
21	chr2:36640800-36647400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:36640800-36651200	Weak transcription	HSMMtube	muscle
23	chr2:36641000-36650000	Weak transcription	NH-A	brain
24	chr2:36641200-36659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:36641400-36647400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:36641400-36647600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:36641400-36650400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:36641600-36651600	Enhancers	Fetal Heart	heart
29	chr2:36642600-36646800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:36643000-36646600	Weak transcription	Small Intestine	intestine
31	chr2:36643800-36646400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:36644000-36648200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:36644200-36647200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:36644200-36647600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr2:36644200-36648400	Weak transcription	Brain Germinal Matrix	brain
36	chr2:36644200-36651400	Weak transcription	Colonic Mucosa	Colon
37	chr2:36644200-36651600	Weak transcription	HMEC	breast
38	chr2:36644200-36657200	Weak transcription	Brain Anterior Caudate	brain
39	chr2:36644200-36660000	Weak transcription	Fetal Brain Female	brain
40	chr2:36644400-36646600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:36644400-36646600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:36644400-36647600	Weak transcription	Brain Angular Gyrus	brain
43	chr2:36644400-36647600	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:36644400-36647600	Weak transcription	Ovary	ovary
45	chr2:36644400-36647600	Weak transcription	Pancreas	Pancrea
46	chr2:36644400-36647600	Weak transcription	Right Atrium	heart
47	chr2:36644400-36647800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:36644400-36649600	Weak transcription	Fetal Kidney	kidney
49	chr2:36644400-36650600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:36644400-36651400	Weak transcription	NHEK	skin

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